rs11411759

Variant names:

• chr5-168062044-CTTT-C
• rs11411759
• NM_001395460.1:c.1310-6_1310-4delTTT

Your query was ambiguous. Multiple possible variants found:

• chr5-168062044-CTTT-C
• chr5-168062044-CTTT-CT
• chr5-168062044-CTTT-CTT
• chr5-168062044-CTTT-CTTTT
• chr5-168062044-CTTT-CTTTTT
• chr5-168062044-CTTT-CTTTTTT
• chr5-168062044-CTTT-CTTTTTTT
• chr5-168062044-CTTT-CTTTTTTTT
• chr5-168062044-CTTT-CTTTTTTTTTT
• chr5-168062044-CTTT-CTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001395460.1(TENM2):​c.1310-6_1310-4delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,333,826 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000025 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TENM2 NM_001395460.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

Genes affected

TENM2 (HGNC:29943): (teneurin transmembrane protein 2) Enables cell adhesion molecule binding activity and signaling receptor binding activity. Involved in several processes, including calcium-mediated signaling using intracellular calcium source; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and retrograde trans-synaptic signaling by trans-synaptic protein complex. Located in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 34 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM2	NM_001395460.1	c.1310-6_1310-4delTTT		splice_region_variant, intron_variant	Intron 8 of 30	ENST00000518659.6	NP_001382389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENM2	ENST00000518659.6	c.1310-15_1310-13delTTT		intron_variant	Intron 8 of 30	5	NM_001395460.1	ENSP00000429430.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 147066 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000255 AC: 34 AN: 1333826 Hom.: 0 AF XY: 0.0000317 AC XY: 21 AN XY: 663068

Gnomad4 AFR exome AF: 0.000100

Gnomad4 AMR exome AF: 0.0000790

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000277

Gnomad4 SAS exome AF: 0.0000777

Gnomad4 FIN exome AF: 0.000126

Gnomad4 NFE exome AF: 0.0000127

Gnomad4 OTH exome AF: 0.0000362

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 147066 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 71304

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11411759; hg19: chr5-167489049;